jalview

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JAL-3641 allow protocol to be configured at top of script

JAL-3641 prototype FASTQ import via groovy script for 2.11.1

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    /examples/groovy/FastQParser.groovy
JAL-3541 ensure deletion of cloverReportDir

JAL-3541 small fix for clover.xml location expected by build server plugin, and comment clarity

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-1889 disable test failing on build server

Merge branch 'bug/JAL-3541_cloverReport_gradle_task_fails' into develop

JAL-3541 added a property/variable style comment to build.gradle

JAL-3624 log when SIFTS mapping fails

Merge branch 'feature/JAL-3624siftsInJS' into develop

JAL-3541 selectively merged build.gradle and gradle.properties

JAL-3626 rescue automatic configuration of JALVIEW_VERSION from the RELEASE properties file, and exclusion of ‘examples’ from the windows installer.

JAL-3621 corrected sequence feature sort and test

JAL-3624 use temp file for SIFT download in JS, correct unmarshalling

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-3463 avoid Thread.sleep() as not supported in SwingJS

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    /src/jalview/ws/DBRefFetcher.java
JAL-3621 update to intervalstore v1.1

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    /j11lib/intervalstore-v1.1.jar
    • binary
    /j8lib/intervalstore-v1.1.jar
JAL-3529 test updated for revised signature of getDBRefs()

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    /test/jalview/io/StockholmFileTest.java
Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/ext/ensembl/EnsemblInfo.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/gui/IdPanel.java
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    /src/jalview/gui/PopupMenu.java
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    /src/jalview/gui/SeqPanel.java
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    /src/jalview/io/StockholmFile.java
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    /src/jalview/util/DBRefUtils.java
  1. … 5 more files in changeset.

changeset discussion

  1. Jim Procter: relevant issue is JAL-3626
JAL-3613 remove debug code committed in error

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    /src/jalview/util/BrowserLauncher.java
JAL-3541 Fixed report path for build artifacts

JAL-3541 Added mem setting and jvmArgs for cloverReporting

JAL-3541 Individual tests now instrumented and reported. Added cloverConsoleReport.

JAL-3541 Helpers for running tests, and other commands headlessly

JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.

    • binary
    /utils/clover/lib/clover-ant-4.4.1.jar
JAL-3613 check sequence overlap when matching search results

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    /src/jalview/datamodel/SearchResults.java
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    • +5
    /src/jalview/util/BrowserLauncher.java
JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used

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    /utils/eclipse/org.eclipse.jdt.ui.prefs
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 add GPL license to Jalview source files

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    /src/jalview/analysis/GeneticCodeI.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/bin/JalviewTaskbar.java
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    /src/jalview/bin/MemorySetting.java
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    /src/jalview/datamodel/GeneLociI.java
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    /src/jalview/datamodel/GeneLocus.java
  1. … 29 more files in changeset.
JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop